Variant rs11546512 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_013283.5(MAT2B):c.525A>G(p.Leu175=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,610,620 control chromosomes in the GnomAD database, including 16,808 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1375 hom., cov: 33)

Exomes 𝑓: 0.14 ( 15433 hom. )

Consequence

MAT2B
NM_013283.5 splice_region, synonymous

Scores

Splicing: ADA: 0.1225

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.30

Variant links:

Genes affected

MAT2B (HGNC:6905): (methionine adenosyltransferase 2 non-catalytic beta subunit) The protein encoded by this gene belongs to the methionine adenosyltransferase (MAT) family. MAT catalyzes the biosynthesis of S-adenosylmethionine from methionine and ATP. This protein is the regulatory beta subunit of MAT. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2012]

MAT2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP7

Synonymous conserved (PhyloP=1.3 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAT2B	NM_013283.5 linkuse as main transcript	c.525A>G	p.Leu175=	splice_region_variant, synonymous_variant	4/7	ENST00000321757.11	NP_037415.1
MAT2B	NM_182796.2 linkuse as main transcript	c.492A>G	p.Leu164=	splice_region_variant, synonymous_variant	4/7		NP_877725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAT2B	ENST00000321757.11 linkuse as main transcript	c.525A>G	p.Leu175=	splice_region_variant, synonymous_variant	4/7	1	NM_013283.5	ENSP00000325425	P1	Q9NZL9-1

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18322

AN:

152134

Hom.:

1376

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0575

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.0123

Gnomad SAS

AF:

0.135

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.104

GnomAD3 exomes

AF:

0.127

AC:

31701

AN:

248896

Hom.:

2478

AF XY:

0.133

AC XY:

17855

AN XY:

134610

show subpopulations

Gnomad AFR exome

AF:

0.0545

Gnomad AMR exome

AF:

0.0647

Gnomad ASJ exome

AF:

0.113

Gnomad EAS exome

AF:

0.00745

Gnomad SAS exome

AF:

0.136

Gnomad FIN exome

AF:

0.218

Gnomad NFE exome

AF:

0.157

Gnomad OTH exome

AF:

0.141

GnomAD4 exome

AF:

0.141

AC:

205337

AN:

1458368

Hom.:

15433

Cov.:

AF XY:

0.142

AC XY:

102808

AN XY:

725480

show subpopulations

Gnomad4 AFR exome

AF:

0.0538

Gnomad4 AMR exome

AF:

0.0676

Gnomad4 ASJ exome

AF:

0.110

Gnomad4 EAS exome

AF:

0.0155

Gnomad4 SAS exome

AF:

0.138

Gnomad4 FIN exome

AF:

0.214

Gnomad4 NFE exome

AF:

0.149

Gnomad4 OTH exome

AF:

0.131

GnomAD4 genome

AF:

0.120

AC:

18321

AN:

152252

Hom.:

1375

Cov.:

AF XY:

0.122

AC XY:

9111

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.0573

Gnomad4 AMR

AF:

0.101

Gnomad4 ASJ

AF:

0.117

Gnomad4 EAS

AF:

0.0123

Gnomad4 SAS

AF:

0.135

Gnomad4 FIN

AF:

0.213

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.105

Alfa

AF:

0.140

Hom.:

1751

Bravo

AF:

0.106

Asia WGS

AF:

0.0920

AC:

322

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.12

dbscSNV1_RF

Benign

0.27

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over